In recent years, developments in the field of life sciences have proceeded at a breathtaking rate. Ground breaking scientific discoveries and advances in such fields as genomics (sequencing and characterization of genetic information and analysis of the relationship between gene activity and cell function) and proteomics (systematic analysis of protein expression in tissues, cells, and biological systems) promise to reshape the fields of medicine, agriculture, and environmental science. The success of these efforts depends, in part, on the development of sophisticated laboratory tools that will automate and expedite the testing and analysis of biological samples.
Current methods of testing typically employ multiple instruments for preparing and analyzing samples and involve multiple manual handling steps and transfers. Such procedures are labor-intensive, time-consuming, and costly and they are susceptible to human error, sample contamination, and loss. After samples have been prepared, they can be subjected to testing procedures that produce data for analysis. Conventional testing procedures often must be performed by an individual laboratory technician, one sample at a time. Laboratory technicians are typically individuals who are most likely trained to operate only a single instrument. Automation will reduce the number of personnel and training necessary to carry out the research. Reliable and accurate automated process and analysis tools are necessary for the benefits of recent scientific discoveries to be fully achieved.
Genomic research is increasing the availability of genomic markers that can be used for the identification of all organisms, including humans. These markers (all genetic loci including SNPs, microsatellites and other noncoding genomic regions) provide a way to not only identify populations but also allow stratification of populations according to their response to drug treatment, resistance to environmental agents, and other factors. Importantly, the identification of the large number of genomic markers has become the driving force behind the development of new automated technologies.
At the forefront of the efforts to develop better analytical tools are efforts to expedite the analysis of complex biochemical structures. For example, robotic devices have been employed to assist in sample preparation and handling.
Such automated sample preparation systems could find application is the areas of: identification and validation of disease-causing genes or drug targets; defining mutations and polymorphisms associated with specific diseases; monitoring gene expression and comparing disease states, cell cycles or other changes; genetic profiling of patients for responsiveness to genomics-based therapies; and genetic profiling of subjects in drug clinical studies to link response with genotype.
The utility of genomic markers to identify and stratify populations is depending on the industry""s ability to measure great numbers (100-100,000) of markers in large populations. This approach is extremely limited in terms of time and research costs. Automation of these systems provides advantages such as increasing throughput and accuracy, but miniaturization also is an important consideration in terms of research costs. Accordingly, there is a need to automate processes in which very small volumes are handled, and retain the accuracy of the results to permit their use in high throughput screening protocols and diagnostics.
Therefore it is an object herein to provide automated systems and methods for high-throughput analysis of biological samples, particularly samples of very small volume, for screening, diagnosis and other procedures. Other objects will become apparent from the following disclosure.
Provided herein is a fully automated modular analytical system that integrates sample preparation, instrumentation, and analysis of biopolymer samples. The samples include, but are not limited to, all biopolymers, e.g., nucleic acids, proteins, peptides, carbohydrates, PNA (peptide nucleic acids), biopolymer (nucleic acid/peptide) analogs, and libraries of combinatorial molecules. The system integrates analytical methods of detection and analysis including but are not limited to, mass spectrometry, radiolabeling, mass tags, chemical tags, fluorescence chemiluminescence, with robotic technology and automated chemical reaction systems to provide a high-throughput, accurate automated process line (APL). The systems and methods provided herein are particularly suited for handling very small volumes, on the order of milliliters, nanoliters and even smaller picoliter volumes.
In certain embodiments, the analytical system includes one portion that is a contamination-controlled environment, such as a clean room or laminar flow room, and includes a means, such as a transporter, for moving the samples from such environment into a second room or space for further processing. This dual space system permits performance of procedures that require clean room conditions to be automatedly linked to procedures that do not require such conditions.
An integrated system for performing a process line comprising a plurality of processing stations, each of which performs a procedure on a biological sample contained in a reaction vessel; a robotic system that transports the reaction vessel from processing station to processing station; a control system that determines when the procedure at each processing station is complete and, in response, moves the reaction vessel to the next test station, and continuously processes reaction vessels one after another until the control system receives a stop instruction; and a data analysis system that receives test results of the process line and automatically processes the test results to make a determination regarding the biological sample in the reaction vessel is provided.
The APL can run unattended continuously with a continuous sample throughput and is capable of analyzing on the order of 10,000-50,000 genotypes per day. The results are highly accurate and reproducible.
Also provided herein are methods for automated analysis of biopolymers using the integrated APL system. In preferred embodiments, provided are automated methods for preparing a biological sample for analysis; introducing the sample into an analytical instrument; recording sample data; automatically processing and interpreting the data; and storing the data in a bioinformatics database. In a particular embodiment, patient DNA samples are automatically analyzed to determine genotype.